HEADER LIGASE 28-MAY-09 2WJP TITLE CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING TITLE 2 RHODANINE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-438; COMPND 5 SYNONYM: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE, D- COMPND 6 GLUTAMIC ACID-ADDING ENZYME, MURD LIGASE; COMPND 7 EC: 6.3.2.9; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 3 ORGANISM_TAXID: 668369; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PABD16/MURD KEYWDS PEPTIDOGLYCAN SYNTHESIS, CELL WALL BIOGENESIS/DEGRADATION, CELL KEYWDS 2 CYCLE, CELL DIVISION, LIGASE, CELL SHAPE SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR T.TOMASIC,N.ZIDAR,R.SINK,A.KOVAC,V.RUPNIK,S.TURK,C.CONTRERAS-MARTEL, AUTHOR 2 A.DESSEN,D.BLANOT,M.MULLER-PREMRU,S.GOBEC,A.ZEGA,L.PETERLIN-MASIC, AUTHOR 3 D.KIKELJ REVDAT 3 13-DEC-23 2WJP 1 REMARK LINK REVDAT 2 26-FEB-14 2WJP 1 SOURCE JRNL REVDAT 1 25-AUG-10 2WJP 0 JRNL AUTH N.ZIDAR,T.TOMASIC,R.SINK,V.RUPNIK,A.KOVAC,S.TURK,D.PATIN, JRNL AUTH 2 D.BLANOT,C.CONTRERAS MARTEL,A.DESSEN,M.MULLER PREMRU,A.ZEGA, JRNL AUTH 3 S.GOBEC,L.PETERLIN MASIC,D.KIKELJ JRNL TITL DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE AND JRNL TITL 2 5-BENZYLIDENETHIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD JRNL TITL 3 LIGASE. JRNL REF J.MED.CHEM. V. 53 6584 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20804196 JRNL DOI 10.1021/JM100285G REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0089 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 72348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3860 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5270 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 266 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3278 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 537 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -0.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.284 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3517 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4788 ; 1.373 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ; 6.576 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;33.223 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 590 ;13.524 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;16.501 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 545 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2667 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2212 ; 2.007 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3550 ; 3.102 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1305 ; 4.620 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1220 ; 7.195 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): -2.9779 60.1834 121.5999 REMARK 3 T TENSOR REMARK 3 T11: 0.0374 T22: 0.0247 REMARK 3 T33: 0.0172 T12: 0.0137 REMARK 3 T13: -0.0089 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.9882 L22: 0.8895 REMARK 3 L33: 0.9263 L12: -0.1464 REMARK 3 L13: 0.3419 L23: -0.6182 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: -0.0322 S13: -0.0067 REMARK 3 S21: -0.0417 S22: 0.0374 S23: -0.0133 REMARK 3 S31: -0.0320 S32: -0.1110 S33: -0.0228 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 93 A 295 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4815 38.0645 132.4978 REMARK 3 T TENSOR REMARK 3 T11: 0.0527 T22: 0.0333 REMARK 3 T33: 0.0370 T12: 0.0057 REMARK 3 T13: 0.0008 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.1203 L22: 0.5329 REMARK 3 L33: 0.3871 L12: -0.1232 REMARK 3 L13: 0.1926 L23: -0.2963 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: -0.0138 S13: 0.0034 REMARK 3 S21: 0.0095 S22: 0.0002 S23: -0.0619 REMARK 3 S31: 0.0256 S32: 0.0018 S33: 0.0145 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 296 A 439 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6945 24.3109 109.8129 REMARK 3 T TENSOR REMARK 3 T11: 0.0428 T22: 0.0075 REMARK 3 T33: 0.0293 T12: -0.0145 REMARK 3 T13: -0.0090 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.9974 L22: 1.9634 REMARK 3 L33: 0.5285 L12: 0.7273 REMARK 3 L13: 0.0340 L23: 0.1483 REMARK 3 S TENSOR REMARK 3 S11: -0.0206 S12: 0.0346 S13: 0.0085 REMARK 3 S21: -0.0930 S22: 0.0495 S23: -0.0388 REMARK 3 S31: 0.0473 S32: -0.0276 S33: -0.0289 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. REMARK 4 REMARK 4 2WJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1290039959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76321 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 46.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 19.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.59000 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3UAG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M (NH4)2SO4, 7% PEG 400, 100 MM REMARK 280 NACL, 100 MM HEPES, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.03150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.01575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.04725 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 222 REMARK 465 ALA A 223 REMARK 465 ASP A 224 REMARK 465 GLU A 225 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 302 N1 AZI A 1445 1.98 REMARK 500 OD1 ASN A 7 O HOH A 2016 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2104 O HOH A 2415 1565 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 13 -122.94 -96.45 REMARK 500 GLN A 243 70.90 50.28 REMARK 500 PHE A 303 53.21 39.93 REMARK 500 ARG A 380 82.76 -161.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 410 PRO A 411 -146.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D17 A 1441 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1442 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 1443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 1444 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 1445 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 1446 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 1447 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1448 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1449 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1450 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1451 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1452 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1453 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1454 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1455 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1456 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1457 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VTD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2UUO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2JFG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP REMARK 900 RELATED ID: 1UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 4UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2JFH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH L-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 3UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2UUP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 1E0D RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2VTE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2JFF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 1EEH RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE DBREF 2WJP A 1 437 UNP P14900 MURD_ECOLI 2 438 SEQADV 2WJP SER A 438 UNP P14900 EXPRESSION TAG SEQADV 2WJP HIS A 439 UNP P14900 EXPRESSION TAG SEQRES 1 A 439 ALA ASP TYR GLN GLY LYS ASN VAL VAL ILE ILE GLY LEU SEQRES 2 A 439 GLY LEU THR GLY LEU SER CYS VAL ASP PHE PHE LEU ALA SEQRES 3 A 439 ARG GLY VAL THR PRO ARG VAL MET ASP THR ARG MET THR SEQRES 4 A 439 PRO PRO GLY LEU ASP LYS LEU PRO GLU ALA VAL GLU ARG SEQRES 5 A 439 HIS THR GLY SER LEU ASN ASP GLU TRP LEU MET ALA ALA SEQRES 6 A 439 ASP LEU ILE VAL ALA SER PRO GLY ILE ALA LEU ALA HIS SEQRES 7 A 439 PRO SER LEU SER ALA ALA ALA ASP ALA GLY ILE GLU ILE SEQRES 8 A 439 VAL GLY ASP ILE GLU LEU PHE CYS ARG GLU ALA GLN ALA SEQRES 9 A 439 PRO ILE VAL ALA ILE THR GLY SER ASN GLY LYS SER THR SEQRES 10 A 439 VAL THR THR LEU VAL GLY GLU MET ALA LYS ALA ALA GLY SEQRES 11 A 439 VAL ASN VAL GLY VAL GLY GLY ASN ILE GLY LEU PRO ALA SEQRES 12 A 439 LEU MET LEU LEU ASP ASP GLU CYS GLU LEU TYR VAL LEU SEQRES 13 A 439 GLU LEU SER SER PHE GLN LEU GLU THR THR SER SER LEU SEQRES 14 A 439 GLN ALA VAL ALA ALA THR ILE LEU ASN VAL THR GLU ASP SEQRES 15 A 439 HIS MET ASP ARG TYR PRO PHE GLY LEU GLN GLN TYR ARG SEQRES 16 A 439 ALA ALA KCX LEU ARG ILE TYR GLU ASN ALA LYS VAL CYS SEQRES 17 A 439 VAL VAL ASN ALA ASP ASP ALA LEU THR MET PRO ILE ARG SEQRES 18 A 439 GLY ALA ASP GLU ARG CYS VAL SER PHE GLY VAL ASN MET SEQRES 19 A 439 GLY ASP TYR HIS LEU ASN HIS GLN GLN GLY GLU THR TRP SEQRES 20 A 439 LEU ARG VAL LYS GLY GLU LYS VAL LEU ASN VAL LYS GLU SEQRES 21 A 439 MET LYS LEU SER GLY GLN HIS ASN TYR THR ASN ALA LEU SEQRES 22 A 439 ALA ALA LEU ALA LEU ALA ASP ALA ALA GLY LEU PRO ARG SEQRES 23 A 439 ALA SER SER LEU LYS ALA LEU THR THR PHE THR GLY LEU SEQRES 24 A 439 PRO HIS ARG PHE GLU VAL VAL LEU GLU HIS ASN GLY VAL SEQRES 25 A 439 ARG TRP ILE ASN ASP SER LYS ALA THR ASN VAL GLY SER SEQRES 26 A 439 THR GLU ALA ALA LEU ASN GLY LEU HIS VAL ASP GLY THR SEQRES 27 A 439 LEU HIS LEU LEU LEU GLY GLY ASP GLY LYS SER ALA ASP SEQRES 28 A 439 PHE SER PRO LEU ALA ARG TYR LEU ASN GLY ASP ASN VAL SEQRES 29 A 439 ARG LEU TYR CYS PHE GLY ARG ASP GLY ALA GLN LEU ALA SEQRES 30 A 439 ALA LEU ARG PRO GLU VAL ALA GLU GLN THR GLU THR MET SEQRES 31 A 439 GLU GLN ALA MET ARG LEU LEU ALA PRO ARG VAL GLN PRO SEQRES 32 A 439 GLY ASP MET VAL LEU LEU SER PRO ALA CYS ALA SER LEU SEQRES 33 A 439 ASP GLN PHE LYS ASN PHE GLU GLN ARG GLY ASN GLU PHE SEQRES 34 A 439 ALA ARG LEU ALA LYS GLU LEU GLY SER HIS MODRES 2WJP KCX A 198 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 198 12 HET D17 A1441 34 HET DMS A1442 4 HET AZI A1443 3 HET AZI A1444 3 HET AZI A1445 3 HET AZI A1446 3 HET AZI A1447 3 HET SO4 A1448 5 HET SO4 A1449 5 HET SO4 A1450 5 HET SO4 A1451 5 HET SO4 A1452 5 HET CL A1453 1 HET CL A1454 1 HET CL A1455 1 HET CL A1456 1 HET CL A1457 1 HET CL A1505 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM D17 N-({3-[({4-[(Z)-(4-OXO-2-THIOXO-1,3-THIAZOLIDIN-5- HETNAM 2 D17 YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-L- HETNAM 3 D17 GLUTAMIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM AZI AZIDE ION HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 D17 C23 H21 N3 O6 S2 FORMUL 3 DMS C2 H6 O S FORMUL 4 AZI 5(N3 1-) FORMUL 9 SO4 5(O4 S 2-) FORMUL 14 CL 6(CL 1-) FORMUL 20 HOH *537(H2 O) HELIX 1 1 LEU A 13 ALA A 26 1 14 HELIX 2 2 GLY A 42 LEU A 46 5 5 HELIX 3 3 ASN A 58 ALA A 64 1 7 HELIX 4 4 HIS A 78 ALA A 87 1 10 HELIX 5 5 GLY A 93 ARG A 100 1 8 HELIX 6 6 GLY A 114 ALA A 129 1 16 HELIX 7 7 PRO A 142 LEU A 147 5 6 HELIX 8 8 SER A 159 THR A 165 1 7 HELIX 9 9 HIS A 183 TYR A 187 5 5 HELIX 10 10 PHE A 189 ALA A 197 1 9 HELIX 11 11 ASP A 214 MET A 218 5 5 HELIX 12 12 LYS A 259 MET A 261 5 3 HELIX 13 13 GLY A 265 ALA A 282 1 18 HELIX 14 14 PRO A 285 PHE A 296 1 12 HELIX 15 15 ASN A 322 ASN A 331 1 10 HELIX 16 16 PHE A 352 LEU A 359 5 8 HELIX 17 17 ASP A 372 ALA A 378 1 7 HELIX 18 18 LEU A 379 GLU A 382 5 4 HELIX 19 19 THR A 389 ALA A 398 1 10 HELIX 20 20 PRO A 399 VAL A 401 5 3 HELIX 21 21 ASN A 421 GLY A 437 1 17 SHEET 1 AA 5 ARG A 52 THR A 54 0 SHEET 2 AA 5 ARG A 32 ASP A 35 1 O VAL A 33 N HIS A 53 SHEET 3 AA 5 VAL A 8 ILE A 11 1 O VAL A 8 N ARG A 32 SHEET 4 AA 5 LEU A 67 ALA A 70 1 O LEU A 67 N VAL A 9 SHEET 5 AA 5 GLU A 90 VAL A 92 1 O GLU A 90 N ILE A 68 SHEET 1 AB 6 VAL A 133 GLY A 137 0 SHEET 2 AB 6 LEU A 153 GLU A 157 1 O LEU A 153 N GLY A 134 SHEET 3 AB 6 ILE A 106 THR A 110 1 O VAL A 107 N LEU A 156 SHEET 4 AB 6 ALA A 173 ILE A 176 1 O ALA A 173 N ALA A 108 SHEET 5 AB 6 CYS A 208 ASN A 211 1 O VAL A 209 N ILE A 176 SHEET 6 AB 6 VAL A 228 PHE A 230 1 O VAL A 228 N VAL A 210 SHEET 1 AC 3 TYR A 237 HIS A 241 0 SHEET 2 AC 3 THR A 246 VAL A 250 -1 O TRP A 247 N ASN A 240 SHEET 3 AC 3 GLU A 253 ASN A 257 -1 O GLU A 253 N VAL A 250 SHEET 1 AD 6 GLU A 304 HIS A 309 0 SHEET 2 AD 6 VAL A 312 ASN A 316 -1 O VAL A 312 N HIS A 309 SHEET 3 AD 6 MET A 406 LEU A 409 1 O VAL A 407 N ILE A 315 SHEET 4 AD 6 LEU A 339 GLY A 344 1 O HIS A 340 N LEU A 408 SHEET 5 AD 6 VAL A 364 PHE A 369 1 O ARG A 365 N LEU A 341 SHEET 6 AD 6 ALA A 384 GLN A 386 1 O GLU A 385 N CYS A 368 SSBOND 1 CYS A 208 CYS A 227 1555 1555 2.07 LINK C ALA A 197 N KCX A 198 1555 1555 1.33 LINK C KCX A 198 N LEU A 199 1555 1555 1.34 SITE 1 AC1 20 ILE A 11 ASP A 35 THR A 36 ARG A 37 SITE 2 AC1 20 SER A 71 PRO A 72 PHE A 161 HIS A 183 SITE 3 AC1 20 LYS A 348 ALA A 414 SER A 415 LEU A 416 SITE 4 AC1 20 ASN A 421 PHE A 422 SO4 A1451 HOH A2525 SITE 5 AC1 20 HOH A2526 HOH A2528 HOH A2529 HOH A2530 SITE 1 AC2 6 GLY A 73 ARG A 186 LEU A 416 HOH A2265 SITE 2 AC2 6 HOH A2529 HOH A2531 SITE 1 AC3 3 ASP A 417 GLN A 418 PHE A 419 SITE 1 AC4 4 ALA A 329 ASN A 331 LEU A 333 HOH A2532 SITE 1 AC5 4 PRO A 300 ARG A 302 PHE A 422 GLU A 423 SITE 1 AC6 2 LEU A 339 ASN A 363 SITE 1 AC7 4 ALA A 102 ALA A 104 PRO A 105 HOH A2164 SITE 1 AC8 8 ASN A 113 GLY A 114 LYS A 115 SER A 116 SITE 2 AC8 8 THR A 117 ARG A 302 HOH A2533 HOH A2534 SITE 1 AC9 6 THR A 166 SER A 167 SER A 168 LEU A 169 SITE 2 AC9 6 ARG A 200 GLU A 203 SITE 1 BC1 4 HIS A 309 ASN A 310 SER A 438 HIS A 439 SITE 1 BC2 8 GLY A 14 LEU A 15 THR A 16 D17 A1441 SITE 2 BC2 8 HOH A2024 HOH A2526 HOH A2535 HOH A2536 SITE 1 BC3 4 ARG A 37 MET A 38 GLN A 170 HOH A2537 SITE 1 BC4 4 HIS A 309 ASN A 310 HOH A2055 HOH A2057 SITE 1 BC5 1 ARG A 395 SITE 1 BC6 3 TYR A 3 GLN A 4 ARG A 27 SITE 1 BC7 4 GLU A 96 THR A 165 SER A 167 HOH A2149 SITE 1 BC8 2 LEU A 57 HOH A2127 CRYST1 65.917 65.917 136.063 90.00 90.00 90.00 P 41 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015171 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015171 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007350 0.00000